Project Summary/Abstract There is a fundamental gap in understanding the genetic contribution to site-specific spontaneous tendon/ligament rupture. The Achilles tendon, rotator cuff, and anterior cruciate ligament are often diseased. Such conditions represent acute damage of a chronically degenerated tendon/ligament. Continued existence of this knowledge gap represents an important problem because, until it is filled, understanding how the large number of genetic variants that contribute to risk of spontaneous tendon/ligament rupture will remain largely incomprehensible. The long-term goal is to discover spontaneous tendon/ligament rupture causal genetic variants. Our overall objective is to discover candidate genetic variants by comprehensive genomic dissection of equine degenerative suspensory ligament desmitis (DSLD), an excellent large animal model of spontaneous tendon/ligament rupture. The genomic architecture of horses acts to increase Power for SNP association by within-breed genome-wide association study (GWAS) as linkage disequilibrium is increased relative to the human genome. The central hypothesis is that DSLD has an important genetic component that is Mendelian. This hypothesis has been formulated on the basis of preliminary data produced in the applicant?s laboratory. The rationale for the proposed research is that knowledge of the genomic architecture underpinning DSLD and discovery of candidate genetic variants in the equine model will enable new and innovative approaches to prevention and treatment of human spontaneous tendon/ligament rupture and also provide a new treatment model. Guided by strong preliminary data, this hypothesis will be tested by pursuing two specific aims: 1) Use RNA sequencing (RNA-Seq) to identify differentially expressed genes in ruptured DSLD tissue and 2) Discover DSLD rupture candidate genetic variants by GWAS and subsequent region-based analysis of whole genome sequence (WGS) data. Under the first aim, differentially expressed genes will be identified by analyzing the transcriptome in diseased tissue to assess disturbances to biological networks. Under the second aim, genomic single nucleotide polymorphisms (SNPs) will be used for discovery GWAS. We will test our working hypothesis that DSLD is a Mendelian disease that is explained by a genetic variant that is shared across DSLD-affected breeds. A shared variant is more likely to be strongly linked to human disease. The work is innovative as it departs from the usual GWAS approach by studying an equine model. New research horizons are expected to be attainable as a result. The proposed research is significant, because it is expected to discover a novel spontaneous tendon/ligament rupture candidate genetic variant and the associated biological pathways. This work will help clarify common pathways that are disturbed in the pathogenesis of spontaneous tendon/ligament rupture. Large effect variants identified in the equine model will provide new targets for preventative or therapeutic management of human patients.